Ivan Alonso's 77th-minute strike saw Nacional cap a relatively dominant performance at the Estadio Gran Parque Central in Montevideo.
Only goal difference separates Nacional and River Plate, who were held to a 1-1 draw at home to El Tanque Sisley.
Lucas Olaza's 81st-minute equaliser helped the league leaders retain their spot at the top after Alejandro Mello's first-half opener.
Danubio missed their chance to go top after being thrashed 3-0 at home to Rentistas.
Gabriel Costa opened the scoring before David Terans struck twice in the space of five second-half minutes.
Despite losing three of their past five league games, Danubio sit third on the table – a point behind the top two.
Liverpool and Miramar Misiones played out a 2-2 draw in an encounter which saw both teams reduced to 10 men.
Sergio Blanco led the way for Wanderers as their six-goal thriller against Racing ended 3-3, with the forward netting a hat-trick.
Cecilio Waterman's dramatic late winner was enough for Fenix to edge Cerro Largo 1-0, while Juventud and Penarol drew 0-0.
Sud America and Defensor Sporting were unable to be separated in a 0-0 draw.
